[BioC] error when using pdInfoBuilder

[James W. MacDonald]

Hi Paul,

On 5/20/2013 2:38 AM, Paul Sanfilippo [guest] wrote:
> Hi,
>
> This is my first attempt at analysing some expression data and I'm having trouble trying to create an annotation package using pdInfoBuilder for some rat array data. I've downloaded the appropriate library files from the affymetrix website, but encounter the following error (which I am unsure how to fix):
>
> Thanks for any suggestions.
>
> Regards,
>
> Paul
>
>
>
>> seed<- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile = clf,probeFile = probe, transFile = trans, coreMps = core)

You might send the results from traceback() after the error. Note that I 
can get this to run, but I am also including the arguments for

author
version
email
organism
species

 > seed <- new("AffyGenePDInfoPkgSeed", pgfFile = fls[29], clfFile = 
fls[27],  coreMps = fls[28], probeFile=fls[30], transFile=fls[32], 
author="James W. MacDonald", email="jmacdon at u.washington.edu", 
biocViews="AnnotationData", organism = "Rat", species = "Rattus norvegicus")
 > makePdInfoPackage(seed, destDir = ".")
================================================================================
Building annotation package for Affymetrix Gene ST Array
PGF.........: RaGene-2_1-st.pgf
CLF.........: RaGene-2_1-st.clf
Probeset....: RaGene-2_1-st-v1.na33.2.rn4.probeset.csv
Transcript..: RaGene-2_1-st-v1.na33.2.rn4.transcript.csv
Core MPS....: RaGene-2_1-st.mps
================================================================================
Parsing file: RaGene-2_1-st.pgf... OK
Parsing file: RaGene-2_1-st.clf... OK
Creating initial table for probes... OK
Creating dictionaries... OK
Parsing file: RaGene-2_1-st-v1.na33.2.rn4.probeset.csv... OK
Parsing file: RaGene-2_1-st.mps... OK
Creating package in ./pd.ragene.2.1.st
Inserting 2640 rows into table chrom_dict... OK
Inserting 5 rows into table level_dict... OK
Inserting 11 rows into table type_dict... OK
Inserting 221214 rows into table core_mps... OK
Inserting 220231 rows into table featureSet... OK
Inserting 675529 rows into table pmfeature... OK
Counting rows in chrom_dict
Counting rows in core_mps
Counting rows in featureSet
Counting rows in level_dict
Counting rows in pmfeature
Counting rows in type_dict
Creating index idx_pmfsetid on pmfeature... OK
Creating index idx_pmfid on pmfeature... OK
Creating index idx_fsfsetid on featureSet... OK
Creating index idx_core_meta_fsetid on core_mps... OK
Creating index idx_core_fsetid on core_mps... OK
Saving DataFrame object for PM.
Saving NetAffx Annotation... OK
Done.

I have the same versions as you.

Best,

Jim



>>
>> makePdInfoPackage(seed, destDir = ".")
> ==========================================================================================================================================================
> Building annotation package for Affymetrix Gene ST Array
> PGF.........: RaGene-2_1-st.pgf
> CLF.........: RaGene-2_1-st.clf
> Probeset....: RaGene-2_1-st-v1.na33.2.rn4.probeset.csv
> Transcript..: RaGene-2_1-st-v1.na33.2.rn4.transcript.csv
> Core MPS....: RaGene-2_1-st.mps
> ==========================================================================================================================================================
> Parsing file: RaGene-2_1-st.pgf... OK
> Parsing file: RaGene-2_1-st.clf... OK
> Creating initial table for probes... Error in .Primitive(":")(dots[[1L]][[1L]], dots[[2L]][[1L]]) :
>    NA/NaN argument
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] pdInfoBuilder_1.24.0 oligo_1.24.0         oligoClasses_1.22.0  affxparser_1.32.0    RSQLite_0.11.3       DBI_0.2-7            Biobase_2.20.0
> [8] BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.28.0         BiocInstaller_1.10.1  Biostrings_2.28.0     bit_1.1-10            codetools_0.2-8       ff_2.2-11
>   [7] foreach_1.4.0         GenomicRanges_1.12.4  IRanges_1.18.1        iterators_1.0.6       preprocessCore_1.22.0 splines_3.0.0
> [13] stats4_3.0.0          tools_3.0.0           zlibbioc_1.6.0
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099